Code for this DE analysis can be found at
maple.sgc.loc/home/bp2582/projects/eye-reg_rnaseq/github/SnailEyeReg_RNASeq/code/DEAnalysis_cond-cutoff.Rmd.
After performing the analysis using as cutoffs adj p-val(FDR) >= 1e-5 and logFC >= |2|, I realized the amount of obtained genes was very little. I don’t think it’s a good idea to loose the pval cutoff since we want to be very confident of the genes we obtain. For that reason, I changed the logFC cutoff to >= 0 in the comparisons that gave us less than 100 genes upregulated or downregulated.
3dpa-intact
6dpa-intact
6dpa-intact
9dpa-intact
12dpa-intact
15dpa-intact
21dpa-intact
28dpa-intact
3dpa-1dpa
6dpa-3dpa
9dpa-6dpa
12dpa-9dpa
15dpa-12dpa
21dpa-15dpa
28dpa-21dpa
intact-28dpa
Can be found at
maple.sgc.loc/home/bp2582/projects/eye-reg_rnaseq/github/SnailEyeReg_RNASeq/data/tables/DEAnalysis/DEGenes/cond-cutoff/de/
Code in
maple.sgc.loc/home/bp2582/projects/eye-reg_rnaseq/github/SnailEyeReg_RNASeq/code/PlotDE-ct_logFC2-1e-5.Rmd.
This list of genes will be used for GO term analysis.